arXiv subjects

Christos N. Likos

Publications and source records attributed to Christos N. Likos.

At least 19 recordsLinked to original sources

arXiv2026

On the design of a profession-oriented course on Theoretical Mechanics for physics education students

We report on a profession-oriented course we offered at the University of Vienna, aimed at physics education teacher students. The course on Theoretical Classical Mechanics has been conceived and designed from its outset with the explicit goal of bridging the gap between the abstract, mathematical notions employed in Theoretical Physics with the concrete future needs of prospective teachers in their profession. We aimed at countering both the negative attitudes of students towards Theoretical Physics and the interrelated skepticism of professors regarding the students mathematical proficiency. Our main findings are that these goals can indeed be achieved through a careful selection of course material and the associated mathematical tools, by closely interwoven lecture topics and exercises, and thorough planning according to principles for high-school teaching known from science education research. Establishing close connections between the material taught in the course and the students future occupation as high-school teachers has proven to be of utmost importance. This is possible without any sacrifice of mathematical rigor or of the quality of Physics presented.

physics.ed-ph↗

arXiv2026

Ion-Modulated Polyelectrolyte Complexation of DNA and Polyacrylic Acid from Molecular Dynamics Simulations

The formation of complexes between like-charged polyelectrolytes challenges conventional electrostatic intuition and highlights the central role of ions in mediating macromolecular organization. Here, we investigate the salt-dependent association of DNA with poly(acrylic acid) (PAA) using atomistic molecular dynamics simulations in NaCl, MgCl$_2$, and CaCl$_2$ solutions. A time-resolved state classification scheme, based on heavy-atom distance and hydrogen-bond formation, was applied to distinguish bound and unbound configurations, enabling quantitative analysis of how ion valency modulates complex stability and structure. The results reveal a clear hierarchy of association strength with Ca$^{2+}$ promoting persistent complex formation through direct inner-sphere coordination between DNA phosphates and PAA carboxylates, Mg$^{2+}$ mediating weaker, transient bridging interactions and Na$^+$ exhibiting only electrostatic screening action with negligible bridge formation. Structural analysis shows that multivalent ions not only enhance complex stability but also reshape the molecular organization of both macromolecules. Ca$^{2+}$ induces expansion of DNA and compaction of PAA within a strongly bridged complex characterized by directional alignment and backbone-dominated binding, whereas Mg$^{2+}$ promotes more transient groove associations and Na$^+$ supports flexible, weakly correlated contacts. Our findings provide molecular-level insight into ion-specific mechanisms underlying polyelectrolyte organization and inform the design of responsive biomaterials and nucleic acid-based assemblies in multivalent ionic environments.

cond-mat.soft↗

arXiv2026

Decoupling of single-particle and collective dynamics in arrested phase-separating glassy mixtures

We investigate the structure and dynamics of a hard colloid-star polymer mixture in the range of its arrested phase separation, where an incipient demixing transition is interfering with a nearby vitrification line, focusing on the protein limit (smaller hard component). Soft-hard mixtures present a rich dynamics, influenced by different parameters such as the concentration of the soft and hard components, the softness of the potential, and the size ratio between the two components. Using coarse-grained molecular dynamics simulations, we characterize the single-particle and collective dynamics of the hard colloidal tracers in the soft glassy matrix. The hard tracers show diffusive behavior of the mean squared displacement accompanied by non-exponential relaxation of the intermediate scattering functions at intermediate length scales and non-Gaussian displacement distributions. Moreover, we show that the system exhibits arrested phase separation, leading to population splitting and decoupling between self- and collective dynamics of the hard colloids. Overall, we demonstrate that the interplay between arrested phase separation and glassiness leads to complex, multiscale phenomena that strongly influence the dynamics of the hard additives in the arrested matrix formed by the soft colloids.

cond-mat.soft↗

arXiv2025

Anisotropic self-assembly of soft particles mediated by elliptically polarized AC fields

Attractive dipole interactions can be induced between equally charged soft nanoparticles under the influence of AC electric fields. The combination of charge repulsion and dipole attraction, along with different screening responses from an underlying electrolyte, lead to complex aggregations ranging from chain-like formation for linear polarizations to isotropic planar structures in the case of circular polarizations. In this work, we analyze the role of varying field anisotropies in these self-assembled structures. To this end, the formalism previously developed for the coarse-grained interactions of soft particles in the presence of linear [T.~Colla {\it et al.}, ACS Nano {\bf 12}, 4321-4337 (2018)] and circular [M.~Reich {\it et al.}, Soft Matter {\bf 21}, 1516-1528 (2025)] field polarizations is naturally extended to incorporate elliptical polarizations of arbitrary asymmetries. A rich variety of self-assembly formations is found at intermediate field anisotropies, thus bridging the gap between linear and circular field-induced self-assembly scenarios.

cond-mat.soft↗

arXiv2025

Locally tuned hydrodynamics of active polymer chains

We employ mesoscopic simulations to study active polymers in a solvent via multi-particle collision dynamics. We investigate linear chains in which either the head or tail monomer exerts an active force, directed away from or towards its neighbor, respectively, while the remaining monomers are passive. We find that, in contrast to flexible chains, for stiff chains the position of the active monomer has minimal influence on both the structural and dynamic properties of the chain. An active head monomer pulls the chain behind it, straightening the backbone -- an effect that can be interpreted as activity-induced stiffening. In contrast, an active tail pushes into the chain, causing crumpling. This leads to faster decorrelation of the polymer backbone over time, rendering the active motion less persistent. These effects occur regardless of whether hydrodynamic interactions are included or not. Hydrodynamics is included by the imposition of a local counter-force in the surrounding fluid, as opposed to distributing the former equally to all fluid elements. By specifying the position of this counterforce onto the fluid, we can tune the hydrodynamic flow fields of the active polymers being both contractile and extensile. Interestingly, the emerging pusher- and puller flow fields are strongly influenced by the force propagation inside the polymer chain.

cond-mat.soft↗

arXiv2024

Entropic tug of war: Topological constraints spontaneously rectify the dynamics of a polymer with heterogeneous fluctuations

Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations to establish directional motion of the chain and corresponding active dynamics. Instead, here we consider an active-passive copolymer, where the two segments differ only by the magnitude of their fluctuations and feature no artificial correlations. Here we show that although the model itself does not possess directional dynamics, if the chains are concentrated, directional persistent motion spontaneously arises as a consequence of the broken translational symmetry owing to the topological constraints. Using scaling arguments and simulations, we explain the phenomenon and describe the ensuing dynamics. Our work has thus far-reaching consequences for the mechanical properties of all dense active polymeric systems with heterogeneous fluctuations and in particular for chromatin conformation and dynamics that are crucial for biological functionality.

cond-mat.soft↗

arXiv2024

Supercoiled ring polymers under shear flow

We apply monomer-resolved computer simulations of supercoiled ring polymers under shear, taking full account of the hydrodynamic interactions, accompanied, in parallel, by simulations in which these are switched off. The combination of bending and torsional rigidities inherent in these polymers, in conjunction with hydrodynamics, has a profound impact on their flow properties. In contrast to their flexible counterparts, which dramatcially deform and inflate under shear [Liebetreu et al., Commun. Mater. 1, 4 (2020)], supercoiled rings undergo only weak changes in their overall shape and they display both a reduced propensity to tumbling (at fixed Weissenberg number) and a much stronger orientational resistance with respect to their flexible counterparts. In the presence of hydrodynamic interactions, the coupling of the polymer to solvent flow is capable of bringing about a topological transformation of writhe to twist at strong shear upon conservation of the overall linking number.

cond-mat.soft↗

arXiv2023

Effects of linking topology on the shear response of connected ring polymers: Catenanes and bonded rings flow differently

We perform computer simulations of mechanically linked (poly[2]catenanes, PC) and chemically bonded (bonded rings, BR) pairs of self-avoiding ring polymers in steady shear. We find that BR's develop a novel motif, termed gradient tumbling, rotating around the gradient axis. For the PC's the rings are stretched and display another new pattern, termed slip-tumbling. The dynamics of BR's is continuous and oscillatory, whereas that of PC's is intermittent between slip-tumbling attempts. Our findings demonstrate the interplay between topology and hydrodynamics in dilute solutions of connected polymers.

cond-mat.soft↗

arXiv2023

Glassy phases of the Gaussian Core Model

We present results from molecular dynamics simulations exploring the supercooled dynamics of the Gaussian Core Model in the low- and intermediate-density regimes. In particular, we discuss the transition from the low-density hard-sphere-like glassy dynamics to the high-density one. The dynamics at low densities is well described by the caging mechanism, giving rise to intermittent dynamics. At high densities, the particles undergo a more continuous motion in which the concept of cage loses its meaning. We elaborate on the idea that these different supercooled dynamics are in fact the precursors of two different glass states.

cond-mat.soft↗

arXiv2021

On the Validity of Effective Potentials in Crowded Solutions of Linear and Ring Polymers with Reversible Bonds

We perform simulations to compute the effective potential between the centers-of-mass of two polymers with reversible bonds. We investigate the influence of the topology of the unbonded precursor (linear or ring) and the specific sequence of the reactive groups (from purely random to periodic), establishing that both have a strong impact on the effective potential. When the reactive sites of both polymers are chemically orthogonal so that only intramolecular bonds are possible, the interactions become more repulsive the closer to periodic the sequence is. The opposite effect is found if both polymers have the same type of reactive sites and intermolecular bonds can be formed. We test the validity of the effective potentials in solution, from high dilution to far above the overlap concentration, by comparing simulations of the effective fluid with those of the real all-monomer system. Very good agreement is found for the reversible linear polymers, indicating that unlike in their non-bonding counterparts many-body effects are minor even far above the overlap concentration. The agreement for the reversible rings is less satisfactory, and at high concentration the real system does not show the clustering behavior predicted by the effective potential. Results similar to the former ones are found for the partial self-correlations in ring/linear mixtures. Finally, we investigate the possibility of creating a gel of two interpenetrated reversible networks. For this purpose we simulate a 50/50 two-component mixture of reversible polymers with orthogonal chemistry for the reactive sites, so that intermolecular bonds are only formed between polymers of the same component. As predicted by both the theoretical phase diagram and the simulations of the effective fluid, the two networks in the all-monomer mixture do not interpenetrate and phase separation (demixing) is observed instead.

cond-mat.soft↗

arXiv2021

Blunt-end driven re-entrant ordering in quasi two-dimensional dispersions of spherical DNA brushes

We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids coated with ultra-long double stranded DNA (dsDNA) fragments reveal non-monotonic particle shrinking, aggregation and re-entrant ordering. Theory and simulations show that shrinking is induced by the osmotic pressure exerted by the counterions absorbed in neighbor brushes, while aggregation and re-entrant ordering are the effect of a short-range attraction competing with the electrostatic repulsion. Blunt-end interactions between dsDNA fragments of neighboring brushes are responsible for the attraction and can be tuned by inducing free-end backfolding through the addition of monovalent salt. Our results show that base stacking is a mode parallel to hybridization to steer colloidal assembly, in which attractions can be fine-tuned through salinity and, potentially, grafting density and temperature.

cond-mat.soft↗

arXiv2021

Physical entanglements mediate coherent motion of the active topological glass confined within a spherical cavity

Motivated by chromosomes enclosed in nucleus and the recently discovered active topological glass, we study a spherically confined melt of long nonconcatenated active polymer rings. Without activity, the rings exhibit the same average large-scale conformational properties as chromatin fiber. Upon activating consecutive monomer segments on the rings, the system arrives at a glassy steady state due to activity-enhanced topological constraints. The latter generate coherent motions of the system, however the resulting large-scale structures are inconsistent with the fractal globule model. We observe microphase separation between active and passive segments without systematic trends in the positioning of active domains within the confining sphere. We find that tank-treading of active segments along the ring contour enhances active-passive phase separation in the state of active topological glass when both diffusional and conformational relaxation of the rings are significantly suppressed. Finally, although the present model of partly-active rings is not compatible with the large-scale chromatin organization, our results suggest that the activity-enhanced entanglements that result in facilitated intra- and inter-chromosomal contacts might be relevant for chromatin structure at smaller scales.

cond-mat.soft↗

arXiv2021

Inverse patchy colloids: synthesis, modeling and self-organization

Inverse patchy colloids are nano- to micro-scale particles with a surface divided into differently charged regions. This class of colloids combines directional, selective bonding with a relatively simple particle design: owing to the competitive interplay between the orientation-dependent attraction and repulsion -- induced by the interactions between like/oppositely charged areas -- experimentally accessible surface patterns are complex enough to favor the stabilization of specific structures of interest. Most important, the behavior of heterogeneously charged units can be ideally controlled by means of external parameters, such as the pH and the salt concentration. We present a concise review about this class of systems, spanning the range from the synthesis of model inverse patchy particles to their self-assembly, covering their coarse-grained modeling and the related numerical/analytical treatments.

cond-mat.soft↗

arXiv2019

Multi-Particle Collision Dynamics for a coarse-grained model of soft colloids

The growing interest in the dynamical properties of colloidal suspensions, both in equilibrium and under an external drive such as shear or pressure flow, requires the development of accurate methods to correctly include hydrodynamic effects due to the suspension in a solvent. In the present work, we generalize Multi-Particle Collision Dynamics (MPCD) to be able to deal with soft, polymeric colloids. Our methods build on the knowledge of the monomer density profile that can be obtained from monomer-resolved simulations without hydrodynamics or from theoretical arguments. We hereby propose two different approaches. The first one simply extends the MPCD method by including in the simulations effective monomers with a given density profile, thus neglecting monomer-monomer interactions. The second one considers the macromolecule as a single penetrable soft colloid (PSC), which is permeated by an inhomogeneous distribution of solvent particles. By defining an appropriate set of rules to control the collision events between the solvent and the soft colloid, both linear and angular momenta are exchanged. We apply these methods to the case of linear chains and star polymers for varying monomer lengths and arm number, respectively, and compare the results for the dynamical properties with those obtained within monomer-resolved simulations. We find that the effective monomer method works well for linear chains, while the PSC method provides very good results for stars. These methods pave the way to extend MPCD treatments to complex macromolecular objects such as microgels or dendrimers and to work with soft colloids at finite concentrations.

cond-mat.soft↗

arXiv2019

Studying synthesis confinement effects on the internal structure of nanogels in computer simulations

We study the effects of droplet finite size on the structure of nanogel particles synthesized by random crosslinking of molecular polymers diluted in nanoemulsions. For this, we use a bead-spring computer model of polymer-like structures that mimics the confined random crosslinking process corresponding to irradiation- or electrochemically-induced crosslinking methods. Our results indicate that random crosslinking under strong confinement can lead to unusual nanogel internal structures, with a central region less dense than the external one, whereas under moderate confinement the resulting structure has a denser central region. We analyze the topology of the polymer networks forming nanogel particles with both types of architectures, their overall structural parameters, their response to the quality of the solvent and compare the cases of non-ionic and ionic systems.

cond-mat.soft↗

arXiv2019

Controlled self-aggregation of polymer-based nanoparticles employing shear flow and magnetic fields

Star polymers with magnetically functionalized end groups are presented as a novel polymeric system whose morphology, self-aggregation, and orientation can easily be tuned by exposing these macromolecules simultaneously to an external magnetic field and to shear forces. Our investigations are based on a specialized simulation technique which faithfully takes into account the hydrodynamic interactions of the surrounding, Newtonian solvent. We find that the combination of magnetic field (including both strength and direction) and shear rate controls the mean number of magnetic clusters, which in turn is largely responsible for the static and dynamic behavior. While some properties are similar to comparable non-magnetic star polymers, others exhibit novel phenomena; examples of the latter include the breakup and reorganization of the clusters beyond a critical shear rate, and a strong dependence of the efficiency with which shear rate is translated into whole-body rotations on the direction of the magnetic field.

cond-mat.soft↗

arXiv2018

Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment

We present a comprehensive theoretical and experimental study of the solution phase properties of DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates, which hold high promise in targeted self-assembly of soft matter systems in the bulk and at interfaces. To describe the behavior of this family of dendrimers (with generations ranging from G1 to G7), we use a theoretical model in which base-pairs of a single DL-DNA molecule are modeled by charged monomers, whose interactions are chosen to mimic the equilibrium properties of DNA correctly. Experimental results on the sizes and conformations of DL-DNA are based on static and 1dynamic light scattering; at the same time, Molecular Dynamics simulations are employed to model the equilibrium properties of DL-DNA, which compare favorably with the findings from experiments while at the same time providing a host of additional information and insight into the molecular structure of the nanostructures. We also examine the salt-responsiveness of these macromolecules, finding that despite the strong screening of electrostatic interactions, brought about by the added salt, the macromolecules shrink only slightly, their size robustness stemming from the high bending rigidity of the DNA-segments. The study of these charged dendrimer systems is an important field of research in the area of soft matter due to their potential role for various interdisciplinary applications, ranging from molecular cages and carriers for drug delivery in a living organism to the development of dendrimer- and dendron-based ultra-thin films in the area of nanotechnology. These findings are essential to determine if DL-DNA is a viable candidate for the experimental realization of cluster crystals in the bulk, a novel form of solids with multiple site occupancy.

cond-mat.soft↗

arXiv2016

Multiblob coarse-graining for mixtures of long polymers and soft colloids

Soft nanocomposites represent both a theoretical and an experimental challenge due to the high number of the microscopic constituents that strongly influence the behaviour of the systems. An effective theoretical description of such systems invokes a reduction of the degrees of freedom to be analysed, hence requiring the introduction of an efficient, quantitative, coarse-grained description. We here report on a novel coarse graining approach based on a set of transferable potentials that quantitatively reproduces properties of mixtures of linear and star-shaped homopolymeric nanocomposites. By renormalizing groups of monomers into a single effective potential between a $f$-functional star polymer and an homopolymer of length $N_0$, and through a scaling argument, it will be shown how a substantial reduction of the to degrees of freedom allows for a full quantitative description of the system. Our methodology is tested upon full monomer simulations for systems of different molecular weight, proving its full predictive potential.

cond-mat.soft↗